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Open Access Publications from the University of California

Robust electron counting for direct electron detectors with the Back-propagation counting method

(2026)

Electron microscopy (EM) is a foundational tool for directly assessing the structure of materials. Recent advances in direct electron detectors have improved signal-to noise ratios via single-electron counting. However, accurately counting electrons at high flux remains challenging. We developed a new method of electron counting for direct electron detectors, Back-Propagation Counting (BPC). BPC uses machine learning techniques designed for mathematical operations on large tensors but does not require large training datasets. In synthetic data, we show BPC is able to count multiple electron strikes per pixel and is robust to increasing occupancy. In experimental data, frames counted with BPC are shown to reconstruct diffraction peaks corresponding to individual nanoparticles with relatively higher intensity and produce images with improved contrast when compared to a standard counting method. Together, these results show that BPC excels in experiments where pixels see a high flux of electron irradiation such as in situ TEM movies and diffraction.

CFD simulation of anisotropic heat transfer and water vapor condensation in gas diffusion layer of a fuel cell

(2026)

Effective water and thermal management are crucial for maximizing the performance of proton exchange membrane fuel cells (PEMFCs). This study presents a robust non-isothermal model that integrates two-phase flow, species transport, and heat and mass transfer phenomena to investigate water generation, accumulation, and permeation mechanisms within the gas diffusion layer (GDL) of PEMFCs. Utilizing X-ray computed tomography (XCT) reconstruction, a 2D structure of the Freudenberg GDL is generated. The model incorporates anisotropic thermal conductivity, distinguishes between in-plane and through-plane K IP K TP ratios, and demonstrates its importance to temperature distribution and subsequent condensation rate within the GDL. Additionally, our parametric analysis evaluates the effects of GDL thermal conductivity, current density, operating temperature, and pressure on water condensation and transport processes in PEMFCs. Key findings include the identification of distinct phases of condensation and transport within the porous medium under varying conditions: nucleation, growth, accumulation, and mobilization. Simulation results uncovered condensation regions within the GDL, demonstrating that temperature gradients, strongly influenced by anisotropic thermal conductivity, play a critical role in water generation and transport dynamics. The study further reveals that areas beneath the land in the GDL exhibit lower temperatures, leading to elevated condensation rates and larger droplet formation within those regions. Additionally, the interconnection of condensate droplets via wetting layers emphasizes the impact of temperature distribution on water movement. This study provides deeper insight into water vapor condensation and transport mechanisms within GDLs, informing the design and optimization of GDL structures for enhanced PEMFC performance.

Cover page of The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy

The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy

(2026)

High-resolution scanning transmission electron microscopy (S/TEM) is an indispensable tool for characterizing the structure and properties of materials down to the atomic scale. Conventional S/TEM imaging, however, is limited by the phase problem, whereby the phase of the electron exit wave is lost upon detection. Recent advances in diffractive imaging and 4D-STEM have enabled a range of phase-retrieval techniques that computationally reconstruct the missing information encoded in the phase of the transmission function. These approaches offer improved dose efficiency and enhanced sensitivity to weakly scattering signals, extending quantitative imaging to beam-sensitive materials composed of light elements. In this work, we introduce the phase problem in electron microscopy and survey the diverse landscape of phase-retrieval techniques used in the field. Despite their many acronyms and algorithmic variations, these techniques share a common physical and mathematical foundation. We present a unified framework that connects these seemingly distinct methods, from parallax imaging and tilt-corrected bright-field (tcBF-STEM), to aberration-corrected bright-field (acBF-STEM), optimum bright-field (OBF-STEM) and single-sideband (SSB) ptychography, as well as first-moment integrated center of mass techniques (iCOM) and iterative ptychographic algorithms. Based on these insights, we discuss the opportunities and practical limitations of applying these methods across different materials systems, detector designs, and microscope configurations.Graphical abstractRepresentative electron microscopy configurations used for phase retrieval and diffractive imaging in S/TEM: (a) Zernike phase-contrast transmission electron microscopy (TEM), (b) small-convergence-angle four-dimensional scanning transmission electron microscopy (4D-STEM) for nanobeam-based phase reconstruction methods, and (c) large-convergence-angle 4D-STEM for ptychographic and related diffractive imaging techniques reviewed in this work.

Cover page of Design and commissioning of a new synchrotron beamline dedicated to X‐ray footprinting mass spectrometry

Design and commissioning of a new synchrotron beamline dedicated to X‐ray footprinting mass spectrometry

(2026)

The structural biology method of X-ray footprinting mass spectrometry (XFMS) is available at two national synchrotron beamlines in the USA: one at the Advanced Light Source (ALS) on the West Coast and the other at the National Synchrotron Light Source II on the East Coast. XFMS is a solution-state technique that utilizes oxidative modifications of proteins at micromolar concentrations in aqueous buffer to extract structural information. X-rays are employed to generate hydroxyl radicals in situ, which covalently modify specific protein side chains. These modifications are subsequently quantified using liquid chromatography and mass spectrometry. Ratiometric changes in modification levels between two protein states (e.g. with and without ligand) generate a relative solvent accessibility map of the protein pairs, which serves to reveal structural features. Up until recently, the XFMS capability was available as part of a shared program at the ALS without a dedicated beamline. In this article, we describe the commissioning of ALS beamline 3.3.1, dedicated to XFMS, including the installation of a new focusing mirror, the design and construction of a new endstation with automated sample handling and exposure capabilities, and the use of accurate empirical dose calculations using Gafchromic film. Finally, we showcase the new beamline capabilities using two protein systems.

Cover page of Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy

Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy

(2026)

Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the atomic scale has been a significant challenge. By utilizing liquid-phase transmission electron microscopy (TEM), we study hydrogen (de)intercalation in palladium nanocrystals as a model system and have achieved unprecedented atomic-resolution imaging of hydrogen intercalation wave dynamics. Our observations reveal that intercalation wave mechanisms, instead of shrinking-core mechanisms, prevail at ambient temperature for palladium nanocubes ranging from ∼60 nm down to ∼10 nm. Systematic image analysis uncovers the atomic evolution of the hydrogen intercalation wave, transitioning from nonplanar and inclined boundaries to those closely aligned with {100} planes. Our kinetic Monte Carlo simulations demonstrate that the observed intercalation wave dynamics correspond to sorption pathways minimizing the lattice mismatch strain at the phase boundary. Unveiling the atomic intercalation pathways holds profound implications for engineering intercalation-mediated devices and advancements in energy sciences.

Cover page of Balancing moisture and oxygen can match the crystallization dynamics of inert halide perovskite processing

Balancing moisture and oxygen can match the crystallization dynamics of inert halide perovskite processing

(2026)

Balancing moisture and oxygen replicates inert crystallization dynamics in antisolvent-free halide perovskite processing under ambient conditions. Understanding crystallization in ambient environments is essential for scaling the fabrication of halide perovskite solar cells. Antisolvent-free perovskite deposition offers improved compatibility with high-throughput processing but introduces distinct crystallization dynamics relative to the more ubiquitous use of antisolvents in lab-scale perovskite fabrication. These dynamics are driven by interactions between solutes, solvent and the deposition environment. Using in situ wide-angle X-ray scattering during spin-coating and annealing, we demonstrate how relative humidity (RH) and oxygen, can be tuned to drive polytype evolution during ambient crystallization of formamidinium lead iodide to match that of inert synthesis and achieve comparable film and device quality. In an inert (N 2 ) environment, we find that perovskite films follow a well-established 2H → 3C phase transformation with a short period of coexistence of the 4H and 6H phase during heating. During crystallization in dry air (RH 0%), the added presence of oxygen leads to the dominance of 4H intermediate for an extended duration, establishing a 2H → 4H → 3C pathway. Introducing low humidity (RH 10%) suppresses the 4H phase to a short-lived intermediate above 100 °C, facilitating a more direct transition to the desired 3C phase and almost replicating the crystallization behavior observed under inert conditions. Interestingly, films crystallized under RH 10% show a lower onset temperature for the perovskite 3C phase than under N 2 . At higher humidity (RH 40%), the strong interaction of oxygen and moisture with iodoplumbates appears to stabilize higher order polytypes (4H and 6H). Devices fabricated under RH 10% achieve higher efficiency and enhanced stability compared to those produced under inert atmosphere. These findings provide mechanistic insight into crystallization pathways in different environments and provide a framework to transfer processes from inert to ambient conditions. The results highlight the critical role of controlled humidity in tuning antisolvent-free perovskite crystallization for scalable processing.

Cover page of Toward Hydrogen Isotope Separations through Strong Hydrogen Adsorption at Open Copper(I) Sites in an Ultramicroporous Metal–Organic Framework

Toward Hydrogen Isotope Separations through Strong Hydrogen Adsorption at Open Copper(I) Sites in an Ultramicroporous Metal–Organic Framework

(2026)

Metal-organic frameworks with coordinatively unsaturated metal sites (open metal sites) capable of engaging in orbital interactions with π-acidic gases are of interest for enabling ambient-temperature gas separations, such as hydrogen isotope separations. In view of the weakly π-acidic nature of H2, we sought to strengthen π-backbonding-mediated H2 adsorption through pore confinement effects. Toward that end, we synthesized and characterized the ultramicroporous metal-organic framework CuxZn5-xCl4-yHz(bbta)3 (CuIZn-MFU-4; H2bbta = 1H,5H-benzo(1,2-d:4,5-d')bistriazole), featuring π-basic trigonal pyramidal CuI sites that reside within 7 Å of one another at their closest. Gas adsorption measurements reveal an H2 adsorption enthalpy of -38 kJ/mol, exceeding that of the larger-pore analog (CuIZn-MFU-4l; -33 kJ/mol) and representing the strongest H2 adsorption yet achieved in a metal-organic framework. The stronger H2 adsorption in CuIZn-MFU-4 is attributed to a combination of pore confinement effects and the increased σ-accepting nature of the CuI sites caused by a more electron-withdrawing bbta2- linker, as supported by structural, spectroscopic, and computational evidence. With the strongest H2 adsorption, equilibrium isotope effects in CuIZn-MFU-4 lead to a D2/H2 selectivity (as estimated by ideal adsorbed solution theory) of 1.35 even at 298 K, approaching the values reported below 200 K for conventional porous materials.

Cover page of Visualizing Millisecond Atomic Dynamics of Nanocrystals in Liquid

Visualizing Millisecond Atomic Dynamics of Nanocrystals in Liquid

(2026)

Atomic structures of nanomaterials are inherently dynamic and continuously reshaped through interactions with chemical species and external stimuli. Such dynamics are further amplified as the size and dimensionality of nanomaterials decrease. Despite advances in analytical methods, it remains challenging to capture the structural dynamics of nanomaterials in reactive environments with both atomic spatial resolution and commensurate temporal resolution. Here, we directly visualize atomic-scale dynamics of gold (Au) nanocrystals in reactive liquid environments with millisecond-speed liquid-cell electron microscopy (EM) and deep-learning denoising. We uncover reversible fluctuations in the local crystallinity of Au nanocrystals dependent on the surrounding chemical environment. These transient fluctuations, driven by interactions at nanocrystal-liquid interfaces, critically influence the dissolution kinetics and grain boundary relaxation. By overcoming the spatiotemporal limitations in conventional liquid-cell EM, our findings provide insights into how transient nanoscale structures dictate the stability and reactivity of nanomaterials.

Cover page of Radiative Electronic Bound States in the Continuum from Defects in Semiconductors

Radiative Electronic Bound States in the Continuum from Defects in Semiconductors

(2026)

Continuum-buried defect states in semiconductors are generally expected to be optically inactive because of their strong coupling to continuum bands. Here, we show that such defects can instead host radiative electronic bound states in the continuum (BICs) using the silicon G center as a prototypical example. Hybrid functional first-principles calculations with a Hubbard U correction reveal that a localized defect state, initially buried below the valence band maximum (VBM) in the ground state, undergoes exchange-driven energy-level reordering under optical excitation and shifts above the VBM. This exchange-induced transition suppresses nonradiative decay and enables a robust radiative emission. By computing temperature-dependent nonradiative lifetimes and comparing them to experimental photoluminescence (PL) lifetimes, we quantitatively reproduce the observed temperature dependence of the emission. These results uncover a stabilization mechanism for continuum-embedded defect states and establish electronic BICs as a general paradigm for designing defect-based optical systems, including quantum emitters and qubits.

Cover page of Visualizing Crystallization Dynamics and Transformation Pathways of Disordered Rocksalt Oxides During Thermally Activated Sol–Gel Synthesis

Visualizing Crystallization Dynamics and Transformation Pathways of Disordered Rocksalt Oxides During Thermally Activated Sol–Gel Synthesis

(2026)

ABSTRACT Sol–gel synthesis is a wet‐chemical processing route for fabricating functional materials with control over composition and microstructure at relatively low temperatures compared to conventional solid‐state synthesis. While sol–gel process initiates with intermixed molecular precursors, the early‐stage nucleation pathways are insufficiently understood. Here, the chemical and structural transformation of disordered rocksalt (DRX) Li 1.2 Mn 0.4 Ti 0.4 O 2 (LMTO), a promising cathode material for lithium batteries, is studied by multiscale characterizations. In situ heating transmission electron microscopy (TEM) using a liquid cell visualizes and identifies crystallization pathways at the nanoscale. While some regions follow a classical multi‐step transition through thermodynamically stable intermediates, others exhibit a kinetic shortcut via a localized amorphous matrix to directly form the DRX structure. Macroscale Fourier transform infrared spectroscopy corroborates the findings and reveals that transition metal ions are more strongly incorporated into the acetate‐coordinated network than lithium. Although in situ heating TEM captures diverse local transformation pathways, in situ synchrotron X‐ray diffraction indicates that the macroscopic transformation proceeds predominantly through spinel LMTO and lithium titanates toward DRX‐LMTO. The findings uncover the spatiotemporal chemical and structural transformations in sol–gel derived DRX‐LMTO materials, and call for fine‐tuning of such sol–gel chemistries to manipulate the crystallization pathways and achieve target material homogeneity more efficiently.